bluecellulab 1.2.5__tar.gz → 1.2.7__tar.gz

{bluecellulab-1.2.5 → bluecellulab-1.2.7}/.gitattributes

@@ -1 +1,2 @@
 *.asc linguist-detectable=false
+*.mod linguist-detectable=false

{bluecellulab-1.2.5 → bluecellulab-1.2.7}/CHANGELOG.rst

@@ -1,6 +1,12 @@
 Changelog
 ==========
 
+1.2.6
+---------
+
+* simplify template loading:remove neuron_release_year<2014 checks
+* make first page of docs the README #48
+
 1.2.0
 -----------
 

{bluecellulab-1.2.5 → bluecellulab-1.2.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 1.2.5
+Version: 1.2.7
 Summary: The Pythonic Blue Brain simulator access
 Home-page: https://github.com/BlueBrain/BlueCelluLab
 Author: Blue Brain Project, EPFL
@@ -65,7 +65,7 @@ Main dependencies
 =================
 
 * `Python 3.8+ <https://www.python.org/downloads/release/python-380/>`_
-* `Neuron 7.4+ <http://neuron.yale.edu/>`_ (compiled with Python support)
+* `Neuron 8.0.2+ <https://pypi.org/project/NEURON/>`_
 
 Installation
 ============

{bluecellulab-1.2.5 → bluecellulab-1.2.7}/README.rst

@@ -46,7 +46,7 @@ Main dependencies
 =================
 
 * `Python 3.8+ <https://www.python.org/downloads/release/python-380/>`_
-* `Neuron 7.4+ <http://neuron.yale.edu/>`_ (compiled with Python support)
+* `Neuron 8.0.2+ <https://pypi.org/project/NEURON/>`_
 
 Installation
 ============

{bluecellulab-1.2.5 → bluecellulab-1.2.7}/bluecellulab/cell/template.py

@@ -15,7 +15,6 @@
 
 from __future__ import annotations
 
-import datetime
 import hashlib
 import os
 from pathlib import Path
@@ -111,45 +110,34 @@ class NeuronTemplate:
         match = re.search(r"begintemplate\s*(\S*)", template_content)
         template_name = match.group(1)  # type:ignore
 
-        neuron_versiondate_string = bluecellulab.neuron.h.nrnversion(4)
-        neuron_versiondate = datetime.datetime.strptime(
-            neuron_versiondate_string, "%Y-%m-%d"
-        ).date()
-        good_neuron_versiondate = datetime.date(2014, 3, 20)
-
-        if neuron_versiondate >= good_neuron_versiondate:
-            logger.info("This Neuron version supports renaming templates, enabling...")
-            # add bluecellulab to the template name, so that we don't interfere with
-            # templates load outside of bluecellulab
-            template_name = "%s_bluecellulab" % template_name
-            template_name = get_neuron_compliant_template_name(template_name)
-            if template_name in cls.used_template_names:
-                new_template_name = template_name
-                while new_template_name in cls.used_template_names:
-                    new_template_name = "%s_x" % new_template_name
-                    new_template_name = get_neuron_compliant_template_name(
-                        new_template_name
-                    )
+        logger.info("This Neuron version supports renaming templates, enabling...")
+        # add bluecellulab to the template name, so that we don't interfere with
+        # templates load outside of bluecellulab
+        template_name = "%s_bluecellulab" % template_name
+        template_name = get_neuron_compliant_template_name(template_name)
+        if template_name in cls.used_template_names:
+            new_template_name = template_name
+            while new_template_name in cls.used_template_names:
+                new_template_name = "%s_x" % new_template_name
+                new_template_name = get_neuron_compliant_template_name(
+                    new_template_name
+                )
 
-                template_name = new_template_name
+            template_name = new_template_name
 
-            cls.used_template_names.add(template_name)
-            template_content = re.sub(
-                r"begintemplate\s*(\S*)",
-                "begintemplate %s" % template_name,
-                template_content,
-            )
-            template_content = re.sub(
-                r"endtemplate\s*(\S*)",
-                "endtemplate %s" % template_name,
-                template_content,
-            )
+        cls.used_template_names.add(template_name)
+        template_content = re.sub(
+            r"begintemplate\s*(\S*)",
+            "begintemplate %s" % template_name,
+            template_content,
+        )
+        template_content = re.sub(
+            r"endtemplate\s*(\S*)",
+            "endtemplate %s" % template_name,
+            template_content,
+        )
 
-            bluecellulab.neuron.h(template_content)
-        else:
-            logger.info("This Neuron version doesn't support renaming "
-                        "templates, disabling...")
-            bluecellulab.neuron.h.load_file(template_filename)
+        bluecellulab.neuron.h(template_content)
 
         return template_name
 

{bluecellulab-1.2.5 → bluecellulab-1.2.7}/bluecellulab/circuit/config/simulation_config.py

@@ -25,7 +25,6 @@ if BLUEPY_AVAILABLE:
     from bluepy_configfile.configfile import BlueConfig
     from bluepy.utils import open_utf8
 from bluepysnap import Simulation as SnapSimulation
-from bluepysnap.circuit_validation import validate as validate_circuit
 
 from bluecellulab.circuit.config.sections import Conditions, ConnectionOverrides
 from bluecellulab.stimuli import Stimulus
@@ -308,10 +307,6 @@ class SonataSimulationConfig:
         else:
             raise TypeError("Invalid config type.")
 
-        # run snap's circuit validation to early detect errors
-        circuit_config_path = self.impl.config["network"]
-        validate_circuit(circuit_config_path, skip_slow=False, only_errors=True)
-
     def get_all_projection_names(self) -> list[str]:
         unique_names = {
             n

{bluecellulab-1.2.5 → bluecellulab-1.2.7}/bluecellulab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 1.2.5
+Version: 1.2.7
 Summary: The Pythonic Blue Brain simulator access
 Home-page: https://github.com/BlueBrain/BlueCelluLab
 Author: Blue Brain Project, EPFL
@@ -65,7 +65,7 @@ Main dependencies
 =================
 
 * `Python 3.8+ <https://www.python.org/downloads/release/python-380/>`_
-* `Neuron 7.4+ <http://neuron.yale.edu/>`_ (compiled with Python support)
+* `Neuron 8.0.2+ <https://pypi.org/project/NEURON/>`_
 
 Installation
 ============

{bluecellulab-1.2.5 → bluecellulab-1.2.7}/bluecellulab.egg-info/SOURCES.txt

@@ -6,7 +6,6 @@
 .zenodo.json
 AUTHORS.txt
 CHANGELOG.rst
-CONTRIBUTORS.txt
 LICENSE
 MANIFEST.in
 Makefile
@@ -79,7 +78,7 @@ docs/source/api.rst
 docs/source/changelog.rst
 docs/source/conf.py
 docs/source/index.rst
-docs/source/_static/.gitignore
+docs/source/_static/.gitkeep
 examples/README.rst
 examples/1-singlecell/singlecell.ipynb
 examples/1-singlecell/hoc/cADpyr_L2TPC.hoc

bluecellulab-1.2.7/docs/source/index.rst

@@ -0,0 +1,16 @@
+.. bluecellulab documentation master file, created by
+   sphinx-quickstart on Mon Jun 19 11:35:51 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+
+.. include:: ../../README.rst
+
+
+.. toctree::
+   :hidden:
+   :maxdepth: 2
+
+   Home <self>
+   api.rst
+   changelog

{bluecellulab-1.2.5 → bluecellulab-1.2.7}/tests/test_cell/test_core.py

@@ -8,7 +8,6 @@ import math
 import random
 import warnings
 from pathlib import Path
-from unittest.mock import patch
 from bluecellulab.circuit.circuit_access import EmodelProperties
 
 import numpy as np
@@ -43,18 +42,6 @@ def test_load_template():
     assert template_name == "test_cell_bluecellulab"
 
 
-@patch("bluecellulab.neuron")
-def test_load_template_with_old_neuron(mock_bluecellulab_neuron):
-    """Test the template loading with an old neuron version."""
-    mock_bluecellulab_neuron.h.nrnversion.return_value = '2014-03-19'
-    fpath = parent_dir / "examples/cell_example1/test_cell.hoc"
-    template_name = NeuronTemplate.load(fpath)
-    assert template_name == "test_cell"
-    mock_bluecellulab_neuron.h.nrnversion.assert_called_once_with(4)
-    mock_bluecellulab_neuron.h.load_file.assert_called_once()
-    mock_bluecellulab_neuron.h.assert_not_called()
-
-
 def test_shorten_and_hash_string():
     """Unit test for the shorten_and_hash_string function."""
     with pytest.raises(ValueError):

bluecellulab-1.2.5/CONTRIBUTORS.txt

@@ -1,20 +0,0 @@
-Contributors
-==================
-
-* Werner Van Geit
-* Anil Tuncel
-* Mike Gevaert
-* Ben Torben Nielsen
-* Eilif Muller
-* Blue Brain HPC Team
-* Alexis Arnaudon
-* Andras Ecker
-* Andrew Hale
-* Arseny Povolotsky
-* Eduard Subert
-* Gianluca Ficarelli
-* Giuseppe Chindemi
-* Joseph Tharayil
-* Liesbeth Vanharpe
-* Pranav Rai
-* Sirio Bolanos Puchet

bluecellulab-1.2.5/docs/source/index.rst

@@ -1,18 +0,0 @@
-.. bluecellulab documentation master file, created by
-   sphinx-quickstart on Mon Jun 19 11:35:51 2023.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-Welcome to bluecellulab's documentation!
-========================================
-
-BlueCelluLab is designed to do simulation and experiment on a single cell or a group of cells. Use cases for which bluecellulab is well suited include: scripting and statistics across single or pairs of cells, light-weight detailed reporting on a few state variables post-simulation, development of synaptic plasticity rules, dynamics validations of e.g. synaptic properties, automation of in-silico whole-cell patching experiments, debugging both scientifically and computationally.
-
-
-.. toctree::
-   :hidden:
-   :maxdepth: 2
-
-   Home <self>
-   api.rst
-   changelog